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Arkadiy-Garber / FeGenie

HMM-based identification and categorization of iron genes and iron gene operons in genomes and metagenomes
GNU Affero General Public License v3.0
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Heatmap has same values regardless of what inflation factor I use #33

Open patrickmon38 opened 2 years ago

patrickmon38 commented 2 years ago

Hi there, and thank you for this tool! I am trying to run some metagenomes through FeGenie and have been successful so far, but I am trying to understand the numbers in FeGenie-heatmap-data.csv a little better. From what I understand, the default is gene counts divided by the predicted number of ORFs for each metagenome, multiplied by 1000. However, I have tried inputting '-inflation 100' (to get a percentage) and '-inflation 1' (to see the raw number), but the output is exactly the same as the default, making me question if I have done something wrong. All of my input files are .fasta, and I am also using the flag '--meta', if that is important. Most of the heatmap numbers are either 0 or in the low hundreds, ranging from 1 to 424.

Any insight would be very helpful. Thanks!

Arkadiy-Garber commented 2 years ago

Hi,

Thanks for your interest in FeGenie. Sorry for the confusion about the -inflation flag. By default, FeGenie does not normalize and provides raw counts of genes. If you want the -inflation argument to have an effect, you will need to invoke the --norm flag, which will force FeGenie to to the normalization with whatever number you set for -inflation. Does this make sense? I will update the help menu to make this feature more clear.

Let me know if you have any other questions or continue to have issues.

Thanks, Arkadiy

patrickmon38 commented 2 years ago

That makes a lot of sense, thank you! I think my main source of confusion was under "Sample command (with more parameters specified)" on the Wiki, '-inflation' is used without '--norm'. I redid my analyses with the --norm flag and it works perfectly. Thank you for your help!